GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Echinicola vietnamensis KMM 6221, DSM 17526

Align Sugar ABC transporter ATP-binding protein (characterized, see rationale)
to candidate Echvi_1022 Echvi_1022 ABC-type spermidine/putrescine transport systems, ATPase components

Query= uniprot:A0A165KQ08
         (355 letters)



>FitnessBrowser__Cola:Echvi_1022
          Length = 345

 Score =  171 bits (434), Expect = 2e-47
 Identities = 97/275 (35%), Positives = 158/275 (57%), Gaps = 14/275 (5%)

Query: 3   SSLDIAGINKRFGKGDKSVEVLRKVDIHVAPGEFLILVGPSGCGKSTLLNIIAGLDEPTE 62
           S L + GI+K+F +  +    ++ + + +  G    +VG +G GK+TLL +IAGL+ P +
Sbjct: 2   SLLQLHGISKKFPQTKQFA--VKDIHMEIEEGSVQAIVGENGSGKTTLLKLIAGLEHPDK 59

Query: 63  GEIRIGGKNVVG----MPPRDRDIAMVFQSYALYPTLSVADNIGFALEMRKMPKPERQKR 118
           GEI   G+ +V     +P   R++ ++FQ YAL+P +++ +N+  AL      +  RQ  
Sbjct: 60  GEIVFSGQTIVNGKSALPANQREVGVIFQEYALFPQMTLLENVREALHQES--RNARQIA 117

Query: 119 IDEVAAMLQISHLLDRRPSQLSGGQRQRVAMGRALARQPQLFLFDEPLSNLDAKLRVEMR 178
           +D +A +  +       P QLS GQRQR A+ RALA +P+L L D+P  +LD + + E+ 
Sbjct: 118 MDSLA-LAGLEDSFSAYPHQLSSGQRQRAALARALASRPKLLLLDDPFRSLDTRFKNEIS 176

Query: 179 AEIKRLHQASGITSVYVTHDQVEAMTLGSRIAVMKGGVVQQLGTPDEIYNRPANTYVATF 238
            +I+ + +A+GIT++  +H   +A++L   IA++  G++QQ+GTP EIY +PAN YVA F
Sbjct: 177 EDIRDIVKATGITAIVASHHAKDALSLADSIAILHKGILQQVGTPVEIYKKPANAYVANF 236

Query: 239 IGSPTMNLLRGAVTGGQFGIQGAALNLAPPPSSAN 273
            G     LL      G +    A     P P SA+
Sbjct: 237 FGKRN-ELLATPTEDGFY----AGFGFIPHPDSAS 266


Lambda     K      H
   0.318    0.135    0.388 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 245
Number of extensions: 9
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 355
Length of database: 345
Length adjustment: 29
Effective length of query: 326
Effective length of database: 316
Effective search space:   103016
Effective search space used:   103016
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory